Main-chain Atoms Research Articles

Principles of peptide selection by the transporter associated with antigen processing

Our ability to fight pathogens relies on major histocompatibility complex class I (MHC-I) molecules presenting diverse antigens on the surface of diseased cells. The transporter associated with antigen processing (TAP) transports nearly the entire repertoire of antigenic peptides into the endoplasmic reticulum for MHC-I loading. How TAP transports peptides specific for MHC-I is unclear. In this study, we used cryo-EM to determine a series of structures of human TAP, both in the absence and presence of peptides with various sequences and lengths. The structures revealed that peptides of eight or nine residues in length bind in a similarly extended conformation, despite having little sequence overlap. We also identified two peptide-anchoring pockets on either side of the transmembrane cavity, each engaging one end of a peptide with primarily main chain atoms. Occupation of both pockets results in a global conformational change in TAP, bringing the two halves of the transporter closer together to prime it for isomerization and ATP hydrolysis. Shorter peptides are able to bind to each pocket separately but are not long enough to bridge the cavity to bind to both simultaneously. Mutations that disrupt hydrogen bonds with the N and C termini of peptides almost abolish MHC-I surface expression. Our findings reveal that TAP functions as a molecular caliper that selects peptides according to length rather than sequence, providing antigen diversity for MHC-I presentation.

Investigating the impact of ultrasound on the structural, physicochemical, and emulsifying characteristics of Dioscorin: Insights from experimental data and molecular dynamics simulation

This study investigated the impact of ultrasound treatment on dioscorin, the primary storage protein found in yam tubers. Three key factors, namely ultrasound power, duration, and frequency, were focused on. The research revealed that ultrasound-induced cavitation effects disrupted non-covalent bonds, resulting in a reduction in α-helix and β-sheet contents, decreased thermal stability, and a decrease in the apparent hydrodynamic diameter (Dh) of dioscorin. Additionally, previously hidden amino acid groups within the molecule became exposed on its surface, resulting in increased surface hydrophobicity (Ho) and zeta-potential. Under specific ultrasound conditions (200 W, 25 kHz, 30 min), Dh decreased while Ho increased, facilitating the adsorption of dioscorin molecules onto the oil-water interface. Molecular dynamics (MD) simulations showed that at lower frequencies and pressures, the structural flexibility of dioscorin's main chain atoms increased, leading to more significant fluctuations between amino acid residues. This transformation improved dioscorin's emulsifying properties and its oil-water interface affinity.

Precise Synthesis of Optically Active and Thermo-degradable Poly(trifluoromethyl methylene) with Circularly Polarized Luminescence.

Developing high performance and environment-friendly fluoropolymers is greatly desired. In this work, we found that 2-diazo-1,1,1-trifluoroethane can be polymerized by air-stable alkyne-palladium(II) catalysts following a living polymerization mechanism, affording a fluoropolymer, poly(trifluoromethyl methylene) in high yield with controlled molar mass and low dispersity. This polymer bears trifluoromethyl on every main chain atom and thus has good resistance to chemical corrosion, high hydrophobicity, and excellent dielectric constant with low dielectric loss. Due to the steric hindrance between the trifluoromethyl pendants, the synthetic poly(trifluoromethyl methylene) can twist into a stable helix. The one-handed preferred helices synthesized using chiral PdII -catalysts exhibit high optical activity and circularly polarized luminescence. Remarkably, such polymer can be completely degraded to (E)-1,1,1,4,4,4-hexafluorobut-2-ene at high temperatures (>280 °C). Additionally, taking advantage of the living chain end, the polymer can be further modified.

Precise Synthesis of Optically Active and Thermo‐degradable Poly(trifluoromethyl methylene) with Circularly Polarized Luminescence

AbstractDeveloping high performance and environment‐friendly fluoropolymers is greatly desired. In this work, we found that 2‐diazo‐1,1,1‐trifluoroethane can be polymerized by air‐stable alkyne‐palladium(II) catalysts following a living polymerization mechanism, affording a fluoropolymer, poly(trifluoromethyl methylene) in high yield with controlled molar mass and low dispersity. This polymer bears trifluoromethyl on every main chain atom and thus has good resistance to chemical corrosion, high hydrophobicity, and excellent dielectric constant with low dielectric loss. Due to the steric hindrance between the trifluoromethyl pendants, the synthetic poly(trifluoromethyl methylene) can twist into a stable helix. The one‐handed preferred helices synthesized using chiral PdII‐catalysts exhibit high optical activity and circularly polarized luminescence. Remarkably, such polymer can be completely degraded to (E)‐1,1,1,4,4,4‐hexafluorobut‐2‐ene at high temperatures (>280 °C). Additionally, taking advantage of the living chain end, the polymer can be further modified.

The crystal structure of the H116Q mutant of NDM-1: An enzyme devoid of zinc ions

New Delhi metallo-β-lactamase 1 (NDM-1) is an important causative factor of antimicrobial resistance due to its efficient hydrolysis of a broad range of β-lactam compounds. The two zinc ions at the active site play essential roles in the NDM-1 catalytic activities. In a previous work, H116, one of the three ligands at the Zn1 site, was mutated in order to investigate the nature of zinc ion chelation. We report here the crystal structure of the NDM-1 H116Q mutant, that was designed to convert a B1 di-zinc enzyme into a B3 type, which either still binds two zinc ions or binds only one at the Zn2 site. The effect of mutation on the overall structure is minimal. Unexpectedly, no zinc ion was observed in the crystal structure. The Zn2-site ligating residue C221 forms a covalent bond with the nearby K121, a residue important in maintaining the active-site structure. The largest conformational changes were found at main-chain and side-chain atoms at residues 232–236 (loop 10), the proper configuration of which is known to be essential for substrate binding. The catalytic-site mutation caused little local changes, yet the effects were amplified and propagated to the substrate binding residues. There were big changes in the ψ angles of residues G232 and L234, which resulted in the side chain of N233 being displaced away from the substrate-binding site. In summary, we failed in turning a B1 enzyme into a B3 enzyme, yet we produced a zinc-less NDM-1 with residual activities.

Metal-induced structural variability of mononuclear metal-binding sites from a database perspective

Metalloproteins are ubiquitous in all kingdoms of life. Their role and function are tightly related to the local structure of the metal-binding site. In this regard, the MetalPDB database is an invaluable tool since it stores the 3D structure of metal-binding sites and of their corresponding apo forms. In this work, we exploited MetalPDB to compute extensive statistics over >3000 clusters of mononuclear sites about the rearrangements occurring upon change in metalation state. For each cluster, we matched the holo and apo sites so that it was possible to average the distances between all possible pairs of Cα and donor atoms and thus quantitatively assess structural variations by computing the Δ values (mean apo distance – mean holo distance). For most of the structures the backbone is rigid with little to no rearrangement, while donor atoms experience significant changes of their relative position when the metal is removed. Sodium and potassium sites are an exception to this general observation. This is most likely caused by their preference for coordination by the main-chain oxygen atoms, making the rearrangement of donor atoms superimposable to that of the backbone. Magnesium and calcium show a different behavior, despite their chemical similarity: calcium sites undergo a larger reorganization upon metalation although both metals have similar percentage of backbone oxygen as donor atoms. We ascribe this observation to the structural and energetic factors regulating the selectivity for calcium over magnesium.

A comparative molecular dynamics and NMR study of H2-Db complex with a Sendai virus antigen reveals the high plasticity of the bound peptide

It has been recognized that different peptides can influence the dynamics of the peptide-loaded MHC-I complex, which plays a pivotal role to CTL recognition and cross reactivity. To gain a deep understanding of the relationship between the peptide-bound MHC-I structure and dynamics we have performed Molecular Dynamics simulations (MDs) of the Sendai virus antigen FAPGNYPAL bound to the mouse allele H2-Db complex with human β2m for an aggregate simulation time of 100 μs. Our MDs predict that the antigenic peptide samples several conformational states with partially dissociated N- and C-termini, mainly as a result of the antigen-binding groove side chain dynamics. These data have been correlated with an NMR study of H2-Db loaded with a series of 13C-labelled FAPGNYPAL and modified pep- tides, which confirmed that the bound peptides sample multiple conformational states. Interestingly, this comparative analysis revealed that peptide dynamics comprising partially dissociated states is not accompanied by large conformational changes of the main chain atoms at the peptide-binding groove of the MHC-I.

The GTP responsiveness of PI5P4Kβ evolved from a compromised trade-off between activity and specificity

Unlike most kinases, phosphatidylinositol 5-phosphate 4-kinase β (PI5P4Kβ) utilizes GTP as a physiological phosphate donor and regulates cell growth under stress (i.e., GTP-dependent stress resilience). However, the genesis and evolution of its GTP responsiveness remain unknown. Here, we reveal that PI5P4Kβ has acquired GTP preference by generating a short dual-nucleotide-recognizing motif called the guanine efficient association (GEA) motif. Comparison of nucleobase recognition with 660 kinases and 128G proteins has uncovered that most kinases and PI5P4Kβ use their main-chain atoms for adenine recognition, while the side-chain atoms are required for guanine recognition. Mutational analysis of the GEA motif revealed that the acquisition of GTP reactivity is accompanied by an extended activity toward inosine triphosphate (ITP) and xanthosine triphosphate (XTP). Along with the evolutionary analysis data that point to strong negative selection of the GEA motif, these results suggest that the GTP responsiveness of PI5P4Kβ has evolved from a compromised trade-off between activity and specificity, underpinning the development of the GTP-dependent stress resilience.

Structural basis for peptide recognition by archaeal oligopeptide permease A.

Oligopeptide permease A (OppA) plays an important role in the nutrition of cells and various signaling processes. In archaea, OppA is a major protein present in membrane vesicles of Thermococcales. Because there being no crystal structures of archaeal OppAs determined to date, we report the crystal structure of archaeal OppA from Thermococcus kodakaraensis (TkOppA) at 2.3Å resolution by the single-wavelength anomalous dispersion method. TkOppA consists of three domains similarly to bacterial OppAs, and the inserted regions not present in bacterial OppAs are at the periphery of the core region. An endogenous pentapeptide was bound in the pocket of domains I and III of TkOppA by hydrogen bonds of main-chain atoms of the peptide and hydrophobic interactions. No hydrogen bonds of side-chain atoms of the peptide were observed; thus, TkOppA may have low peptide selectivity but some preference for residues 2 and 3. TkOppA has a relatively large pocket and can bind a nonapeptide; therefore, it is suitable for the binding of large peptides similarly to OppAs of Gram-positive bacteria.

The importance of residue-level filtering and the Top2018 best-parts dataset of high-quality protein residues.

We have curated a high-quality, "best-parts" reference dataset of about 3 million protein residues in about 15,000 PDB-format coordinate files, each containing only residues with good electron density support for a physically acceptable model conformation. The resulting prefiltered data typically contain the entire core of each chain, in quite long continuous fragments. Each reference file is a single protein chain, and the total set of files were selected for low redundancy, high resolution, good MolProbity score, and other chain-level criteria. Then each residue was critically tested for adequate local map quality to firmly support its conformation, which must also be free of serious clashes or covalent-geometry outliers. The resulting Top2018 prefiltered datasets have been released on the Zenodo online web service and are freely available for all uses under a Creative Commons license. Currently, one dataset is residue filtered on main chain plus Cβ atoms, and a second dataset is full-residue filtered; each is available at four different sequence-identity levels. Here, we illustrate both statistics and examples that show the beneficial consequences of residue-level filtering. That process is necessary because even the best of structures contain a few highly disordered local regions with poor density and low-confidence conformations that should not be included in reference data. Therefore, the open distribution of these very large, prefiltered reference datasets constitutes a notable advance for structural bioinformatics and the fields that depend upon it.

Cp(π-Allyl)Pd-Initiated Polymerization of Diazoacetates: Reaction Development, Kinetic Study, and Chain Transfer with Alcohols

A new initiating system, (cyclopentadienyl) (π-allyl)palladium(II) [Cp(π-allyl)Pd], for the polymerization of diazoacetate monomers has been developed. Homo- and copolymers bearing an ester substituent at every main-chain carbon atom were efficiently synthesized from various alkyl and aryl diazoacetates. In particular, this polymerization system can tolerate various functional groups, which allows for effective postpolymerization functionalization of the resultant polymers. Detailed kinetic study indicates that this polymerization has the characteristics of slow initiation and rapid propagation. Furthermore, alcohols were found to function as chain transfer agents as confirmed by polymerization experiments and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) analyses of the polymer products, thus providing an effective method for controlling the molecular weight of the polymer.

Virulence effector SidJ evolution in Legionella pneumophila is driven by positive selection and intragenic recombination.

Effector proteins translocated by the Dot/Icm type IV secretion system determine the virulence of Legionella pneumophila (L. pneumophila). Among these effectors, members of the SidE family (SidEs) regulate several cellular processes through a unique phosphoribosyl ubiquitination mechanism mediated by another effector, SidJ. Host-cell calmodulin (CaM) activates SidJ to glutamylate the SidEs of ubiquitin (Ub) ligases and to make a balanced Ub ligase activity. Given the central role of SidJ in this regulatory process, studying the nature of evolution of sidJ is important to understand the virulence of L. pneumophila and the interaction between the bacteria and its hosts. By studying sidJ from a large number of L. pneumophila strains and using various molecular evolution algorithms, we demonstrated that intragenic recombination drove the evolution of sidJ and contributed to sidJ diversification. Additionally, we showed that four codons of sidJ which are located in the N-terminal (NTD) (codons 58 and 200) and C-terminal (CTD) (codons 868 and 869) domains, but not in the kinase domain (KD) had been subjected to strong positive selection pressure, and variable mutation profiles of these codons were identified. Protein structural modeling of SidJ provided possible explanations for these mutations. Codons 868 and 869 mutations might engage in regulating the interactions of SidJ with CaM through hydrogen bonds and affect the CaM docking to SidJ. Mutation in codon 58 of SidJ might affect the distribution of main-chain atoms that are associated with the interaction with CaM. In contrast, mutations in codon 200 might influence the α-helix stability in the NTD. These mutations might be important to balance Ub ligase activity for different L. pneumophila hosts. This study first reported that intragenic recombination and positive Darwinian selection both shaped the genetic plasticity of sidJ, contributing to a deeper understanding of the adaptive mechanisms of this intracellular bacterium to different hosts.

Two Methods, One Goal: Structural Differences between Cocrystallization and Crystal Soaking to Discover Ligand Binding Poses.

In lead optimization, protein crystallography is an indispensable tool to analyze drug binding. Binding modes and non‐covalent interaction inventories are essential to design follow‐up synthesis candidates. Two protocols are commonly applied to produce protein–ligand complexes: cocrystallization and soaking. Because of its time and cost effectiveness, soaking is the more popular method. Taking eight ligand hinge binders of protein kinase A, we demonstrate that cocrystallization is superior. Particularly for flexible proteins, such as kinases, and larger ligands cocrystallization captures more reliable the correct binding pose and induced protein adaptations. The geometrical discrepancies between soaking and cocrystallization appear smaller for fragment‐sized ligands. For larger flexible ligands that trigger conformational changes of the protein, soaking can be misleading and underestimates the number of possible polar interactions due to inadequate, highly impaired positions of protein amino‐acid side and main chain atoms. Thus, if applicable cocrystallization should be the gold standard to study protein–ligand complexes.

Role of Thermolysin in Catalytic-Controlled Self-Assembly of Fmoc-Dipeptides

In recent years, short peptide self-assembled materials, prepared under the control of the thermolysin catalyst, have been investigated extensively and shown to acquire various morphologies and fun...

Discovery of a series of benzopyrimidodiazepinone TNK2 inhibitors via scaffold morphing

The protein kinase TNK2 (ACK1) is an emerging drug target for a variety of indications, in particular for cancer where it plays a key role transmitting cell survival, growth and proliferative signals via modification of multiple downstream effectors by unique tyrosine phosphorylation events. Scaffold morphing based on our previous TNK2 inhibitor XMD8-87 identified urea 17 from which we developed the potent and selective compound 32. A co-crystal structure was obtained showing 32 interacting primarily with the main chain atoms of an alanine residue of the hinge region. Additional H-bonds exist between the urea NHs and the Thr205 and Asp270 residues.

Predicting protein model correctness in Coot using machine learning.

Manually identifying and correcting errors in protein models can be a slow process, but improvements in validation tools and automated model-building software can contribute to reducing this burden. This article presents a new correctness score that is produced by combining multiple sources of information using a neural network. The residues in 639 automatically built models were marked as correct or incorrect by comparing them with the coordinates deposited in the PDB. A number of features were also calculated for each residue using Coot, including map-to-model correlation, density values, B factors, clashes, Ramachandran scores, rotamer scores and resolution. Two neural networks were created using these features as inputs: one to predict the correctness of main-chain atoms and the other for side chains. The 639 structures were split into 511 that were used to train the neural networks and 128 that were used to test performance. The predicted correctness scores could correctly categorize 92.3% of the main-chain atoms and 87.6% of the side chains. A Coot ML Correctness script was written to display the scores in a graphical user interface as well as for the automatic pruning of chains, residues and side chains with low scores. The automatic pruning function was added to the CCP4i2 Buccaneer automated model-building pipeline, leading to significant improvements, especially for high-resolution structures.

Identification of the Structure of Polybutadiene Terminal Units by NMR Spectroscopy with T2-Filter

A new method for the identification of the structure of terminal units in polybutadiene synthesized by cationic polymerization has been developed. The method consists of conducting T2-filtered NMR experiments, which make it possible to reduce the intensities of the spectral signals of the main-chain carbon atoms and significantly increase the intensities of the signals of the carbon atoms in the head and end polybutadiene units characterized by higher mobility.

ALEPH: a network-oriented approach for the generation of fragment-based libraries and for structure interpretation.

The analysis of large structural databases reveals general features and relationships among proteins, providing useful insight. A different approach is required to characterize ubiquitous secondary-structure elements, where flexibility is essential in order to capture small local differences. The ALEPH software is optimized for the analysis and the extraction of small protein folds by relying on their geometry rather than on their sequence. The annotation of the structural variability of a given fold provides valuable information for fragment-based molecular-replacement methods, in which testing alternative model hypotheses can succeed in solving difficult structures when no homology models are available or are successful. ARCIMBOLDO_BORGES combines the use of composite secondary-structure elements as a search model with density modification and tracing to reveal the rest of the structure when both steps are successful. This phasing method relies on general fold libraries describing variations around a given pattern of β-sheets and helices extracted using ALEPH. The program introduces characteristic vectors defined from the main-chain atoms as a way to describe the geometrical properties of the structure. ALEPH encodes structural properties in a graph network, the exploration of which allows secondary-structure annotation, decomposition of a structure into small compact folds, generation of libraries of models representing a variation ofa given fold and finally superposition of these folds onto a target structure. These functions are available through a graphical interface designed to interactively show the results of structure manipulation, annotation, fold decomposition, clustering and library generation. ALEPH can produce pictures of the graphs, structures and folds for publication purposes.

Ultrasound-assisted extraction ameliorates the physicochemical properties of defatted mulberry seed protein to promote lipid production in Schizochytrium sp. SR21

To improve protein extraction rate and the utilization of mulberry seed protein (MSP) for biorefinery purposes, ultrasound-assisted extraction was used to treating defatted mulberry seed protein (DMSP) for enhancing lipid production in Schizochytrium sp. SR21. Under ultrasound irradiation with solid-liquid ratio of 1:40, temperature of 60 °C, time of 9 min, and output power of 600 W, the extraction rate of DMSP reached 77.05%, which was significantly improved than the blank control (18.70%) and microwave treatment (22.50%). Moreover, the solubility and emulsibility of DMSP treated by ultrasound were significantly improved; the assay results measured by near-infrared Raman Spectroscopy showed that ultrasound-assisted treatment could reduce the α-helix in the protein (reduced by 9.75%); correspondingly, structures of β-sheet and β-turn increased 1.33% and 3.01%; it indicated that ultrasound treatment changed the spatial arrangement of protein main chain atoms. The antioxidant activity test and the amino acid composition of defatted mulberry seed protein hydrolysate (DMSPH) showed that ultrasound-assisted treatment enhanced the antioxidant activity of the protein hydrolysate and there was no significant difference in amino acid composition between the DMSP and yeast extract. The DMSPH was used as nitrogen source to cultivate Schizochytrium sp. SR21 which showed that DMSPH promoted lipid production and the DHA content was 35.55%, which was better than the results of cultured with traditional nitrogen source; it indicates that DMSP can be used as nitrogen source in culture of microorganisms and further explanation of ultrasound-assisted treatment of modified MSP as an alternative nitrogen source achieved the goal of biorefinery.

α-Actinin-1 promotes activity of the L-type Ca2+ channel Cav 1.2.

The L-type Ca2+ channel CaV 1.2 governs gene expression, cardiac contraction, and neuronal activity. Binding of α-actinin to the IQ motif of CaV 1.2 supports its surface localization and postsynaptic targeting in neurons. We report a bi-functional mechanism that restricts CaV 1.2 activity to its target sites. We solved separate NMR structures of the IQ motif (residues 1,646-1,664) bound to α-actinin-1 and to apo-calmodulin (apoCaM). The CaV 1.2 K1647A and Y1649A mutations, which impair α-actinin-1 but not apoCaM binding, but not the F1658A and K1662E mutations, which impair apoCaM but not α-actinin-1 binding, decreased single-channel open probability, gating charge movement, and its coupling to channel opening. Thus, α-actinin recruits CaV 1.2 to defined surface regions and simultaneously boosts its open probability so that CaV 1.2 is mostly active when appropriately localized.